Colin Kaepernick didn’t play that badly in the 49ers’ third exhibition game. Watching him complete just half his passes, you didn’t want to poke a pencil into your eye or stick your finger down your throat. Give him that.

He threw some good passes. He really did. Early in the second quarter, he went on a roll — sort of. He hit LaMichael (Peanut) James for seven yards, whipped a bullet to Vernon Davis for 16, threw a laser past a defender to Michael Crabtree for 10 and checked down to Bruce Miller for seven yards. Four plays in a row just like that. All of it was nifty work, what you’d expect from the Niners’ starting quarterback, a player who is not yet elite but hopes to be.

That mini-roll gives the team and the fans hope the offense isn’t a dud. The 49ers should have a very good defense, but so far the offense — we’re talking the first-team offense — has verged on dud. Call it dormant with a chance of waking up at a date to be determined.

Take what happened right after Kaepernick’s mini-roll. He handed the ball to running back Carlos Hyde — lots of potential in that guy — and Hyde ran hard up the middle for nine. That put the ball at the 17-yard line of the San Diego Chargers. That put the ball in the red zone, the Niners’ danger zone. What would they ever do?

Here’s what they did. On first down, a defender deflected Kaepernick’s pass to Quinton Patton. On second down, Peanut ran up the middle and lost four. On third down, Kaepernick threw short left to Vance McDonald and missed him. Then the 49ers kicked a field goal. The usual.

After that series, his fourth, the 49ers took Kaepernick out of the game, but not before he reasserted certain truths about his play.

1) He still is no genius in the red zone.

2) He still has thrown no touchdown passes this preseason, as in none.

Why is it bad to throw no TD passes in Exhibition Game 3?

Because Game 3 is the closest to a real game in this silly prelude to the season. Teams do a certain amount of trying. Kaepernick certainly tried to score from the red zone, but couldn’t. Does this mean the 49ers’ offense is no good? It does not mean that. It means it has work to do.

This we do know. Kaepernick’s offensive line — an area of concern for the team — did not protect the rich young quarterback. The Niners have not adequately replaced guard Alex Boone whose holdout has lasted so long it has become a lifestyle. The Niners have not adequately replaced center Jonathan Goodwin, now with the Saints. And right tackle Anthony Davis has played no plays this preseason because of injury.

According to my count, Kaepernick took four big hits in the first three offensive series. Call them brain-rattlers. Once, he fumbled the ball but the officials didn’t call it a fumble. Then he took another rattler and fumbled for real and the Chargers recovered.

I believe Jim Harbaugh would have left Kaepernick and the first-string offense in longer than four series so it actually could score a touchdown. But he was scared stiff Kaepernick would get murdered before the sellout crowd and, although scoring a TD would be good for the morale of the offense, instant death to Kaepernick would be a blow to the team’s collective ego.

When Kaepernick left the game, his passer rating was 64.2, a substandard number. By comparison, San Diego’s Philip Rivers had a rating of 135.4, twice as good as Kaepernick’s.

Numbers can be inconclusive and it’s not the aim of this column to say Kaepernick is a 64.2 guy. But for what it’s worth — and it’s worth something — the 49ers’ offense under Kaepernick did not improve this preseason. Come to think of it, he didn’t improve either.

It’s easy and almost irrelevant to argue whether Blaine Gabbert is a suitable backup quarterback. Gabbert played well enough on Sunday — 110.4 passer rating. But he is someone you write about and talk about and think about only in preseason. He is not the starting quarterback. Kaepernick is. Kaepernick matters to the future of the 49ers and Gabbert does not. And Kaepernick has been no big deal through three games.

Afterward, Kaepernick came to the interview auditorium where he spoke for about three minutes.

Listen in:

Q: How do you evaluate the first-team offense?

A: We have some things to improve on before we get to the season.

Q: Such as?

A: Execution.

Q: You didn’t have a lot of time to throw. What was the issue?

A: Execution. We have good plays. We just didn’t execute.

At which point, I chimed in, “You said it’s execution. Is this about average for how you execute in the third game? Are you beyond what you usually do or maybe a little behind?

Kaepernick: That’s tough to say. I don’t know what the standard would be to say whether we’re better or not.

Cohn: But you play. I don’t play. You must actually be aware of the standard.

Kaepernick: To our standards?

Cohn: Yeah.

Kaepernick: This was below.

Cohn: Below?

Kaepernick: Yeah.

Cohn: Does that concern you?

Kaepernick: No, it’s preseason.

What did we learn from this little dialogue which we can only describe as football meets postmodernism? I’m thinking Harold Pinter or Samuel Beckett. We learned Kaepernick doesn’t like to give a straight answer to a straight question. We learned he will give a straight answer if you persist, if you wade through the verbal obstacles. He finally admitted the offense is below standard.

We appreciate Kaepernick’s candor. We admire how he says much in few words. We call this verbal “precision,” one of Harbaugh’s favorite words. We say Kaepernick’s play must be as precise as his talking — fast, careful economical, sharp, to the point, no wasted effort.

When Kaepernick plays like he talks, he and the offense will be season ready. Execution.

Yes i agree, the 49er offense has been terrrible. But this is not a story until if and when it happens in the regular season. Also, since when did you get so obsessed with QB ratings? Does Blaine gabbert’s QB rating in a preseason game against a bunch of scrubs actually matter to you? Pretty pointless stuff.

One fans take (mine): the preseason games have been concerning. But 1 good showing against Dallas and all will be forgotten. Some guys, like Kaepernick, are “big game guys”. They rise to the occasion and elevate their play through passion. Conversely when the end result doesn’t matter, they slouch their way through. I believe this applies to Iupati and I suspect Stevie Johnson as well. Patton is another passionate performer but he’s still so green that preseason gets his juice flowing. If you’ve played in 2 conference championships and 1 Super Bowl in 2 years, preseason likely doesn’t move the needle.

The good news for SF fans is that some of the young guys are flashing talent. Borland, Lynch, Ward, Hyde and Vance made exciting plays. Preseason is their time because the young players are competing with each other for the opportunity to play in the games that matter.

So while we all feel anxious waiting to see if Colin and company can turn it on, at least we have evidence that the draft produced some exciting players.

You see the Seahawks come out each preseason game and Russell Wilson throws 20 or so passes, completes 15 abd the starting unit utterly dominates.
You see the Niners flounder. Repeatedly.
At best, it’s ” it’s only preseason”.
Moderately, its “well, they’re the Niners, we haven’t seen them really showing anything yet”.
Frighteningly, it’s “oh-oh!”
What concerns me most is that the passing game does not look anything different than what they’ve run for years.

we may set a league record for FGs. no team makes getting a 1st down appear so difficult. the rules are set up for effortless yardage and scoring.

SF & Stanford in Pac 12 eschew the traditional (current tradition) in favor of something contrary. this works well in postseason. I find it inherently risky in reg season.

any game we play versus an ARodgers / Romo / Brees / Rivers / Manning(s) / Brady etc will be a game we can very easily lose given the preference for methodical offense.

I fear SF over estimates the value of young player as well. The young players on defense will pay big dividends this yr as Bowmand and Smith can best be replaced for maybe half the season by waves of young talent.

the offense feels systemically deficient. the 2nd half of 2012 is the best template for 2014, and we remember how that ended.

It is horrifying to admit that both NYG & Balt have won SBs while SF has had this tremendous resurgence with top players in prime. last yr was probably an out performance, and probably best augurs for this yr being no different (with young replacement making big contributions).

trouble now is that SEA is loaded, and appears ahead of the curve on all levels. they won with star RB avg just 4ypc and Wilson not dominating yet, and no Harvin.

we scored 40 TDs last yr and prob need at least 8 more this yr to stay level presuming defense yields more pts. i would bet on SEA evolving this much yr over yr than SF on offense, and further suspect SEA remains superior to SF on defense.

bummer. timing could not be worse for blowing 2011 NFCCG and SB the following yr. by time we get even if ever to SEA our window may look smaller. at best window looks less certain after NFCCG last yr in SEA.

I refuse to get my undies in a bunch over preseason games. Lowell has to because he needs something to write about. Now if they look this bad against the Cowboys and lose then we will have something to concern ourselves with. But until then, calm down and enjoy Lowell’s writing. “The Niners have not adequately replaced guard Alex Boone whose holdout has lasted so long it has become a lifestyle.” You have got to love that!

I don’t understand why the media gives Roman a free pass, if this was Chicago or New York, he would be under attack. Roman will never get a Head Coaching position in the NFL, even if we win the Super Bowl. Actually I don’t think he can even get another Offensive coordinator position with another team, other then the Niners.

Got to appreciate Lowel Cohn, telling it the way it is, asking the tough questions, and daring to mention the sacred elephant in the room who has no clothes on. Everyone over-protects our QB, excusing him for everything while ignorantly believing his problems are with his receivers, not with himself.